[BioC] P calls (VSN and RMA)

[Isaac Neuhaus]

We agree with Rafael that using algorithms such as VSN and RMA greatly 
reduces the noise at the lower intensities (hurray!). However, there is 
still the biological fact that a lot of the probesets on any chip assay 
genes that are not expressed in the cell type being tested. 
Incorporating the null measurements for these probesets greatly affects 
any kind of multiple test corrections applied in analysis of the data.

For this reason, we would also really like to filter out these 
unexpressed genes. One way is simply using an intensity cut, but this 
seems arbitrary, unless it is genuinely linked to detection ability of 
the technology.  Does anyone have comments or ideas?

Petra and Isaac



Rafael A. Irizarry wrote:

>in my opinionm the main reason affy uses these is because MAS 5.0 has so
>much noise at "the bottom". if they didnt, all their large fold changes
>would be for genes with low expression. with RMA, what i use, you dont
>have this problem so i dont see the need to throw away information. there
>are other ways to get rid of the "noise" at the bottom: dChip (pm-only)
>and vsn are two exaples.
>
>There is no designated place to stick them into exprSet. you could create
>another exprSet just for these or since MAS doesnt give SEs,
>you could stick them in the se.exprs slot. a better (but you need to code
>some) solution is to extend the exprSet class to a new class that includes
>a slot for these calls.
>
>On Mon, 17 Mar 2003, Stephen Henderson wrote:
>
>  
>
>>I'd like to use the Present (P) and Absent (A) calls for some rudimentary
>>filtering of data prior to analysis. Is there an appropriate slot for
>>inserting P and A calls within the exprSet object? 
>>
>>I'd like to garner opinions: Does anyone else use these , think them
>>worthwhile, or perhaps use some other surrogate? 
>>
>>
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